{ "_id": "6a10476eacfb0bcc41c9ef28", "Package": "GSReg", "Version": "1.47.0", "Date": "2016-11-28", "Title": "Gene Set Regulation (GS-Reg)", "Author": "Bahman Afsari , Elana J. Fertig\n", "Maintainer": "Bahman Afsari , Elana J. Fertig\n", "Description": "A package for gene set analysis based on the variability\nof expressions as well as a method to detect Alternative\nSplicing Events . It implements DIfferential RAnk Conservation\n(DIRAC) and gene set Expression Variation Analysis (EVA)\nmethods. For detecting Differentially Spliced genes, it\nprovides an implementation of the Spliced-EVA (SEVA).", "License": "GPL-2", "biocViews": "GeneRegulation, Pathways, GeneExpression,\nGeneticVariability, GeneSetEnrichment, AlternativeSplicing", "Config/pak/sysreqs": "make libbz2-dev liblzma-dev libpng-dev libxml2-dev\nlibssl-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:39:25 UTC", "RemoteUrl": "https://github.com/bioc/GSReg", "RemoteRef": "HEAD", "RemoteSha": "8a97f7bb28e0561b3f1e8796357c3755bebf2bfd", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-10 09:35:55 UTC", "User": "root" }, "MD5sum": "b6cc82c1a2157296da6c86dfa963ff92", "_user": "bioc", "_type": "src", "_file": "GSReg_1.47.0.tar.gz", "_fileid": "3888323d327f09e078c7180f41354813f0518f2ccb3a6ec0bdf6cf463af8c46f", "_filesize": 594058, "_sha256": "3888323d327f09e078c7180f41354813f0518f2ccb3a6ec0bdf6cf463af8c46f", "_created": "2026-05-10T09:35:55.000Z", "_published": "2026-05-22T12:09:18.666Z", "_jobs": [ { "job": 77376137697, "time": 266, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "6902731026" }, { "job": 77376138202, "time": 317, "config": "linux-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "6902736368" }, { "job": 77376137919, "time": 408, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "6902744809" }, { "job": 77376138258, "time": 299, "config": "linux-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "6902734503" }, { "job": 77376138262, "time": 389, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "6902743773" }, { "job": 77376138199, "time": 281, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "6902838557" }, { "job": 77376138229, "time": 449, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "6902761931" }, { "job": 77376137833, "time": 189, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "6902828888" }, { "job": 77376137933, "time": 387, "config": "macos-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "6902757205" }, { "job": 77376137035, "time": 370, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "6902703765" }, { "job": 77376137276, "time": 231, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7160113445" }, { "job": 77376137854, "time": 438, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "6902747802" }, { "job": 77376138286, "time": 424, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "6902746454" }, { "job": 77376137654, "time": 398, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "6902744021" } ], "_bioccheck": { "error": 1, "warning": 2, "note": 13 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/25625238113", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/GSReg", "_commit": { "id": "8a97f7bb28e0561b3f1e8796357c3755bebf2bfd", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777379965 }, "_maintainer": { "name": "Bahman Afsari", "email": "ejfertig@jhmi.edu", "login": "afsari", "uuid": 2557586 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 2.13.1", "role": "Depends" }, { "package": "Homo.sapiens", "role": "Depends" }, { "package": "org.Hs.eg.db", "role": "Depends" }, { "package": "GenomicFeatures", "role": "Depends" }, { "package": "AnnotationDbi", "role": "Depends" }, { "package": "GenomicRanges", "role": "Suggests" }, { "package": "GSBenchMark", "role": "Suggests" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "1.47.0", "bioc": "3.24" }, { "branch": "release", "version": "1.46.0", "bioc": "3.23" } ], "_topics": [ "generegulation", "pathways", "geneexpression", "geneticvariability", "genesetenrichment", "alternativesplicing" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 346, "source": "https://www.bioconductor.org/packages/stats/bioc/GSReg" }, "_mentions": 3, "_searchresults": 23, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/GSReg.html", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_exports": [ "GSReg.GeneSets.DIRAC", "GSReg.GeneSets.EVA", "GSReg.kendall.tau.distance", "GSReg.kendall.tau.distance.restricted", "GSReg.kendall.tau.distance.template", "GSReg.overlapJunction", "GSReg.SEVA" ], "_datasets": [ { "name": "geneExrsGSReg", "title": "", "object": "juncExprsSimulated", "file": "juncExprsSimulated.rda", "class": [ "matrix", "array" ], "fields": [ "sample_01_N", "sample_02_N", "sample_03_N", "sample_04_N", "sample_05_N", "sample_06_N", "sample_07_N", "sample_08_N", "sample_09_N", "sample_10_N", "sample_11_N", "sample_12_N", "sample_13_N", "sample_14_N", "sample_15_N", "sample_16_N", "sample_17_N", "sample_18_N", "sample_19_N", "sample_20_N", "sample_21_N", "sample_22_N", "sample_23_N", "sample_24_N", "sample_25_N", "sample_01_T", "sample_02_T", "sample_03_T", "sample_04_T", "sample_05_T", "sample_06_T", "sample_07_T", "sample_08_T", "sample_09_T", "sample_10_T", "sample_36_T", "sample_37_T", "sample_38_T", "sample_39_T", "sample_40_T", "sample_41_T", "sample_42_T", "sample_43_T", "sample_44_T", "sample_45_T", "sample_46_T", "sample_47_T", "sample_48_T", "sample_49_T", "sample_50_T" ], "rows": 20, "table": true, "tojson": true }, { "name": "junc.RPM.Simulated", "title": "", "object": "juncExprsSimulated", "file": "juncExprsSimulated.rda", "class": [ "matrix", "array" ], "fields": [ "sample_01_N", "sample_02_N", "sample_03_N", "sample_04_N", "sample_05_N", "sample_06_N", "sample_07_N", "sample_08_N", "sample_09_N", "sample_10_N", "sample_11_N", "sample_12_N", "sample_13_N", "sample_14_N", "sample_15_N", "sample_16_N", "sample_17_N", "sample_18_N", "sample_19_N", "sample_20_N", "sample_21_N", "sample_22_N", "sample_23_N", "sample_24_N", "sample_25_N", "sample_01_T", "sample_02_T", "sample_03_T", "sample_04_T", "sample_05_T", "sample_06_T", "sample_07_T", "sample_08_T", "sample_09_T", "sample_10_T", "sample_36_T", "sample_37_T", "sample_38_T", "sample_39_T", "sample_40_T", "sample_41_T", "sample_42_T", "sample_43_T", "sample_44_T", "sample_45_T", "sample_46_T", "sample_47_T", "sample_48_T", "sample_49_T", "sample_50_T" ], "rows": 242, "table": true, "tojson": true }, { "name": "phenotypes", "title": "", "object": "juncExprsSimulated", "file": "juncExprsSimulated.rda", "class": [ "factor" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "GSReg-package", "title": "A package for Gene Set Analysis based on the variability of gene expression in different phenotypes.", "topics": [ "GSReg-package", "GSReg" ] }, { "page": "GSReg_GeneSets_DIRAC", "title": "Performs DIRAC for gene set analysis from the paper Eddy et al (2010).", "topics": [ "GSReg.GeneSets.DIRAC" ] }, { "page": "GSReg_GeneSets_VReg.", "title": "Performs Gene Set Analysis using Expression Variation Analysis (EVA).", "topics": [ "GSReg.GeneSets.EVA" ] }, { "page": "GSReg_Kendall", "title": "Calculate Kendall-tau distance in different forms", "topics": [ "GSReg.kendall.tau.distance", "GSReg.kendall.tau.distance.restricted", "GSReg.kendall.tau.template" ] }, { "page": "GSReg_OverlapJunction", "title": "Generates junction overlap matrices required for SEVA", "topics": [ "GSReg.overlapJunction" ] }, { "page": "GSReg_SEVA", "title": "Applies Splice-EVA (SEVA) algorithm", "topics": [ "GSReg.SEVA" ] } ], "_rundeps": [ "abind", "AnnotationDbi", "askpass", "BH", "Biobase", "BiocBaseUtils", "BiocGenerics", "BiocIO", "BiocManager", "BiocParallel", "Biostrings", "bit", "bit64", "bitops", "blob", "cachem", "cigarillo", "cli", "codetools", "cpp11", "crayon", "curl", "DBI", "DelayedArray", "fastmap", "formatR", "futile.logger", "futile.options", "generics", "GenomicAlignments", "GenomicFeatures", "GenomicRanges", "glue", "GO.db", "graph", "Homo.sapiens", "httr", "IRanges", "jsonlite", "KEGGREST", "lambda.r", "lattice", "lifecycle", "Matrix", "MatrixGenerics", "matrixStats", "memoise", "mime", "openssl", "org.Hs.eg.db", "OrganismDbi", "pkgconfig", "png", "R6", "RBGL", "RCurl", "restfulr", "Rhtslib", "rjson", "rlang", "Rsamtools", "RSQLite", "rtracklayer", "S4Arrays", "S4Vectors", "Seqinfo", "snow", "SparseArray", "SummarizedExperiment", "sys", "TxDb.Hsapiens.UCSC.hg19.knownGene", "vctrs", "XML", "XVector", "yaml" ], "_vignettes": [ { "source": "GSReg.Rnw", "filename": "GSReg.pdf", "title": "Working with the GSReg package", "engine": "utils::Sweave", "headings": [], "created": "2014-07-17 23:30:16", "modified": "2018-11-16 19:30:29", "commits": 5 } ], "_score": 4.139879086401237, "_indexed": true, "_nocasepkg": "gsreg", "_universes": [ "bioc", "afsari" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.47.0", "date": "2026-05-10T09:40:08.000Z", "distro": "noble", "arch": "aarch64", "commit": "8a97f7bb28e0561b3f1e8796357c3755bebf2bfd", "fileid": "bee0a3813eb3a49578808ac2b963e0fe8265b1af7386f629f48a326920498b2d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25625238113" }, { "r": "4.7.0", "os": "linux", "version": "1.47.0", "date": "2026-05-10T09:41:10.000Z", "distro": "noble", "arch": "x86_64", "commit": "8a97f7bb28e0561b3f1e8796357c3755bebf2bfd", "fileid": "b5c97feca324b5acaa4ff348f5d479b5f5f6089c8c1baaa366dcbac6a0e77ad1", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25625238113" }, { "r": "4.6.0", "os": "linux", "version": "1.47.0", "date": "2026-05-10T09:39:53.000Z", "distro": "noble", "arch": "aarch64", "commit": "8a97f7bb28e0561b3f1e8796357c3755bebf2bfd", "fileid": "eeb211ffe78c456edb6b963570436813a2635b24769df8d3a260085de1e8c75d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25625238113" }, { "r": "4.6.0", "os": "linux", "version": "1.47.0", "date": "2026-05-10T09:41:09.000Z", "distro": "noble", "arch": "x86_64", "commit": "8a97f7bb28e0561b3f1e8796357c3755bebf2bfd", "fileid": "8c25521158f792153c3a5a31ce0dc95ffad9a244ce699bb9c3a9d8003f79c233", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25625238113" }, { "r": "4.5.3", "os": "mac", "version": "1.47.0", "date": "2026-05-10T09:57:56.000Z", "arch": "aarch64", "commit": "8a97f7bb28e0561b3f1e8796357c3755bebf2bfd", "fileid": "1db324ec1521e3315d8c8943b79ba07ecf119cb3064995bfc57a2493f07edec0", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25625238113" }, { "r": "4.5.3", "os": "mac", "version": "1.47.0", "date": "2026-05-10T09:43:40.000Z", "arch": "x86_64", "commit": "8a97f7bb28e0561b3f1e8796357c3755bebf2bfd", "fileid": "63d102c210bdab98300f800a94ec7103f5a9b098892f47a9f5d49a0bbe1efd1b", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25625238113" }, { "r": "4.6.0", "os": "mac", "version": "1.47.0", "date": "2026-05-10T09:56:52.000Z", "arch": "aarch64", "commit": "8a97f7bb28e0561b3f1e8796357c3755bebf2bfd", "fileid": "59e15a4bccb809eaff14d945c3f5e125bff5c0b1eac07286cec4a09cb0bb707d", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25625238113" }, { "r": "4.6.0", "os": "mac", "version": "1.47.0", "date": "2026-05-10T09:42:52.000Z", "arch": "x86_64", "commit": "8a97f7bb28e0561b3f1e8796357c3755bebf2bfd", "fileid": "fce86c7bda0f0d654a608cf55e66939fa01a06509890966694141953274b4abe", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25625238113" }, { "r": "4.7.0", "os": "win", "version": "1.47.0", "date": "2026-05-10T09:41:41.000Z", "arch": "x86_64", "commit": "8a97f7bb28e0561b3f1e8796357c3755bebf2bfd", "fileid": "fb1ee0ddab3f769572109319b97016271fb293f464061ce1960e01c1af1f4604", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25625238113" }, { "r": "4.5.3", "os": "win", "version": "1.47.0", "date": "2026-05-10T09:41:29.000Z", "arch": "x86_64", "commit": "8a97f7bb28e0561b3f1e8796357c3755bebf2bfd", "fileid": "350cae68fdc17092c867df3dc3a6051dab5c850fcbac28a55599904db4e403b3", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25625238113" }, { "r": "4.6.0", "os": "win", "version": "1.47.0", "date": "2026-05-10T09:41:06.000Z", "arch": "x86_64", "commit": "8a97f7bb28e0561b3f1e8796357c3755bebf2bfd", "fileid": "3aa9da621e9cdc7c16c3f360ac7d6c7ade56e3aa756e10e77a821f85d974c691", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25625238113" }, { "r": "4.6.0", "os": "wasm", "version": "1.47.0", "date": "2026-05-22T12:08:46.000Z", "arch": "emscripten", "commit": "8a97f7bb28e0561b3f1e8796357c3755bebf2bfd", "fileid": "e1c354b5049215b9ae2e21fdd878c5073f4139152fc9689fa410bece1267f0c7", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/25625238113" } ] }